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. 2014 Aug;8(8):1577-87.
doi: 10.1038/ismej.2014.17. Epub 2014 Feb 20.

Taxonomical and functional microbial community selection in soybean rhizosphere

Lucas W Mendes  1 , Eiko E Kuramae  2 , Acácio A Navarrete  1 , Johannes A van Veen  3 , Siu M Tsai  4
Affiliations

Taxonomical and functional microbial community selection in soybean rhizosphere

"VSports app下载" Lucas W Mendes et al. ISME J. 2014 Aug.

Abstract

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils VSports手机版. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. .

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Figures

Figure 1
Figure 1
NMDS of Bray–Curtis similarity matrix among 24 samples from mesocosms experiments with soybean. Taxonomic (a) and functional (b) analyses using relative abundance based on SEED bacterial matches at the phylum level and subsystem level 2. The lines between dots represent the minimal spanning tree, which connects all points with minimal total length, based on similarity index. Stress values are shown in the upper right of the graphs. Similarity values (analysis of similarity) are shown in the down right of each plot.
Figure 2
Figure 2
Relative abundance of bacteria at the phylum level based on shotgun metagenomics data. Percentage of total sequence reads in samples from bulk soil and rhizosphere of 1-year and 5-year of soybean harvesting is presented here for the 2 years of experiments (I and II). The error bars show calculated standard variation of triplicate samples, and asterisks (*) indicate more abundant phyla in rhizosphere (P-value<0.05). Corrected P-values were calculated using the Benjamini–Hochberg false discovery rate approach (P<0.05).
Figure 3
Figure 3
Relative abundance of functional categories (SEED subsystem level 1) based on shotgun metagenomics data. Percentage of total sequence reads in samples from bulk soil and rhizosphere of 1-year and 5-year of soybean harvesting is presented here for the 2 years of experiments (I and II). The error bars show calculated standard variation of triplicate samples and asterisks (*) indicate categories more abundant in rhizosphere (P-value<0.05). Corrected P-values were calculated using the Benjamini–Hochberg false discovery rate approach (P<0.05).
Figure 4
Figure 4
Network of bulk soil and rhizosphere based on correlation analysis from taxonomic and functional profiles. A connection stands for strong (Spearman's r>0.7) and significant (P<0.01) correlation. Red nodes indicate taxonomic affiliation at class level, and blue nodes indicate functional categories based on subsystems at level 2 (SEED Database). The size of each node is proportional to the number of connections. The numbers inside red nodes indicate the phyla with more correlations, as follows: (1) Deltaproteobacteria; (2) Bacteroidetes; (3) Chloroflexi; (4) Planctomycetacia; (5) Sphingobacteria; (6) Solibacteres; and (7) Gammaproteobacteria.
Figure 5
Figure 5
Comparison of taxonomic profile between 1-year (light green) and 5-year (dark green) soybean rhizosphere samples. (a) Scatter plot showing differences at order level (P<0.05). (b) Scatter plot showing differences at the family level (P<0.05). (c) Differences in phylum abundance between 1-year and 5-year rhizosphere samples for the 2 years of experiments (I and II). Corrected P-values were calculated using the Benjamini–Hochberg false discovery rate approach (P<0.05).
Figure 6
Figure 6
Comparison of functional profile between 1-year (light green) and 5-year (dark green) soybean rhizosphere samples. (a) Scatter plot showing differences for protein metabolism (SEED level 2). (b) Scatter plot showing differences for regulation and cell signaling (SEED level 2). (c) Functional groups (SEED level 1) statistically different between 1-year and 5-year rhizosphere. Corrected P-values were calculated using the Benjamini–Hochberg false discovery rate approach (P<0.05).
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